Multiple sequence alignment by
MAFFT
ver.5.743
I / O
Input
:
Paste protein or DNA sequences in fasta format.
Example
or upload a file:
I have protein structural alignment(s).
New!
Help
(OPTIONAL) Structural alignment 1
(Used as constraints as far as consistent with other structural alignments):
Help
Paste a protein alignment in fasta format.
Example
(OPTIONAL) Structural alignment 2
:
Paste a protein alignment in fasta format.
(OPTIONAL) Structural alignment 3
:
Paste a protein alignment in fasta format.
(OPTIONAL) Structural alignment 4
:
Paste a protein alignment in fasta format.
Output
:
Email to
Web
Output order
:
Same as input
Aligned
Advanced settings
Strategy
:
FFT-NS-1 (Very fast; recommended for >2000 sequences; progressive method)
FFT-NS-2 (Fast; progressive method)
(Medium; iterative refinement method, two cycles only)
FFT-NS-i (Slow; iterative refinement method)
L-INS-i (Very slow; recommended for <200 sequences)
Help
E-INS-i (Very slow; recommended for <200 sequences)
Help
Parameters
:
Scoring matrix (for amino acid sequences):
BLOSUM30
BLOSUM45
BLOSUM62
BLOSUM80
JTT100
JTT200
Gap opening penalty:
(1.0-3.0)
Offset value:
(0.0-1.0; functions like gap extension penalty)